Just catching up here, so please forgive if you have learned anything in the meantime, but hopefully this helps.
The IGMM will always mark the external mods with a triangle to show they are "third party", it doesn't necessarily mean
they are bad, especially if you can load in, it just means that it is seeing them.
Not all the mods available on Nexus will be on Mod.io/IGMM, some are not even able to be moved over.
If you are trying to load into a previous save, that is potentially from prior to patch 7- your best bet would be to roll
back to a previous patch the old fashioned way.
If you are okay with starting over and new, you should vanilla your game, clean out all files and folders, run it to make
sure everything is smooth and then slowly start adding newer mods, one at a time. Patch 7 has a LOT of content, so if
you are adding in mods, especially if they are outdated or unoptimized, you are going to run your PC into the ground.
